[gmx-users] how to understand the sentence

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 12 03:13:22 CET 2006

nk yx wrote:
> Hi all,
>      When I am reading the  help list of "grompp" , I find a sentence 
> which says "For an exact restart do not forget to turn off velocity 
> generation and turn on
> unconstrained starting when constraints are present in the system".      
> I donot understand the half latter sentence. I try to understand it as 
> follow:
> I finished a 5ns MD simulation,and then I want to continue to run 
> another 5 ns MD for certain reason. When I use the grompp to generate 
> the continue.tpr , I need set "constraint=none" in the continue.tpr file 
> since in the first.tpr I have set "constraint=all-bonds/h-bonds".
>  Am I right? Hope to get some hints from you all. Thanks in advance.

There is a run control option (described in 7.3.17 Bonds) called
unconstrained_start that does this for you. You should leave
constraint=all-bonds (or whatever) the same. Better still is to use
"tpbconv -extend" to convert the old .tpr to one suitable for
continuting the run. Check out the tpbconv manpage for details.

For background, when using SHAKE/LINCS/whatever there are bond length
constraints that need to be enforced, but if you leave
unconstrained_start = yes, gromacs will attempt to enforce them at the
end of the old run and again at the start of the new run, which isn't
what you want.


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